The present invention relates generally to compositions and methods for detecting nucleic acids for the organism Borrelia burgdorferi in a test sample.
The following discussion of the background of the invention is merely provided to aid the reader in understanding the invention and is not admitted to describe or constitute prior art to the present invention.
Lyme disease, also known as Lyme borreliosis, is a tick-transmitted, spirochetal, inflammatory disorder causing a rash (erythema [chronicum] migrans) that may be followed weeks to months later by neurologic, cardiac, or joint abnormalities. Lyme disease was recognized in 1975 because of close clustering of cases in Lyme, Conn. It has since been reported in many states in USA and numerous foreign countries.
Lyme disease has been the most commonly reported tick-borne illness in the USA. It is caused by a spirochete, Borrelia burgdorferi, transmitted primarily by minute ticks of the ixodes ricinus complex. Once attached to the skin, they continue to engorge on blood for days. Transmission of Borrelia burgdorferi does not usually occur until the infected tick has been in place for at least 36 to 48 hrs; thus, screening for ticks after potential exposure and removing them can help prevent infection.
Borrelia burgdorferi enters the skin at the site of the tick bite. It may spread in lymph, producing regional adenopathy, or disseminate in blood to organs or other skin sites. The relative paucity of organism in the involved tissue suggests that most manifestations of infection are due to host immune response rather than to the destructive properties of the organisms.
Patients with Lyme disease suffer from a variety of chronic and acute syndromes caused by Borrelia burgdorferi. The signs and symptoms of Lyme disease vary over time and between individuals. The characteristic clinical manifestation following the bite of an infected tick is a distinctive skin rash, erythema migrans, which often occurs in conjunction with mild constitutional symptoms. Later stages of Lyme disease may include severe arthritic, neurological, and cardiac manifestations.
The diagnosis of Lyme disease is made by clinical examination combined with evidence of tick bite or exposure in endemic areas, and this usually coincides with evidence of seroreactivity to the organism. Diagnosis of early Lyme disease in a patient with typical erythema migrans in an endemic area does not require laboratory confirmation. Titers of specific antispirochetal antibodies (first IgM, then IgG) can be determined by ELISA or by indirect immunofluorescence, but are not useful before the patient has made antibodies. Confirmation of positive titers by Western blot is also needed. In addition, false- positive results can be high. Thus, testing is best reserved for patients in whom suspicion is high. Moreover, serological testing does not recognize the presence of the spirochete itself, but rather the host""s immunological response to the organism following a recent or past infection. Culture of Borrelia burgdorferi from blood and other body tissues is possible, but the recovery rate is low, and it may require many weeks before growth of the organism is evident.
The polymerase chain reaction (PCR) provides a sensitive and specific means of detecting the presence of Borrelia burgdorferi in clinical specimens, and it has been used successfully to detect Borrelia burgdorferi in body fluids including blood. See, e.g., (Benach et al., N. Engl. J. Med. 308: 740-742, 1983); serum (Liebling et al., Arth Rheum 36: 665-675, 1993); cerebral spinal fluid and synovial fluid (Liebling et al., Arth Rheum 36: 665-675, 1993); and in urine (Schmidt et al., Diagn. Microbiol. Infect. Dis. 21: 121-128, 1995). A diagnosis of Borrelia burgdorferi infections using a real-time PCR assay is also reported (Schwaiger et al., Clin. Microbiol. Infect. 7(9): 461-9, 2001).
The present invention provides methods and compositions for determining the presence and/or amount of Borrelia burgdorferi nucleic acids in a test sample. In particular, substantially purified oligonucleotides for qualitatively and/or quantitatively detecting Borrelia burgdorferi nucleic acids in a test sample by amplification methods are described herein. The present invention can provide a specific, sensitive method that can exhibit a broad dynamic range of detection of Borrelia burgdorferi nucleic acids.
In various embodiments of the present invention, oligonucleotide primers and probes are used in the methods described herein to provide the Borrelia burgdorferi assay. Thus, in certain embodiments, the invention relates to primer sequences that can be used to amplify FlaA gene in the Borrelia burgdorferi gene sequence present in a sample. The FlaA gene in the Borrelia burgdorferi gene sequence encodes the flagellin protein. In addition, primers can also be used to amplify one or more control nucleic acid sequences. Control amplification primers may contain only control-specific sequences, or may be hybrid primers that can amplify the control sequence(s) while simultaneously introducing FlaA gene sequences into the control amplicon produced. By introducing FlaA gene sequences into the control amplicon, the control can be introduced into test samples and amplified by the same primers used to amplify the target FlaA gene in the Borrelia burgdorferi gene sequences, providing a convenient positive control.
In additional embodiments, the invention relates in part to probe nucleic acids that can be conjugated to a detectable label, preferably, a fluorescent dye, and most preferably a dye pair located at the 5xe2x80x2 and 3xe2x80x2 end of the oligonucleotides. Certain labeled oligonucleotides are described that hybridize to amplified FlaA gene in the Borrelia burgdorferi gene sequences, if present, in the sample. Similarly, certain labeled oligonucleotides are described that hybridize to a control amplicon that may have been introduced into the test sample as a positive control.
In a first aspect, the invention relates to one or more substantially purified oligonucleotides having sequences selected from the following group:
5xe2x80x2-TTG CAA ATC TTT TCT CTG GTG-3xe2x80x2 (SEQ ID NO:1), a Fla A gene sequence;
5xe2x80x2-AGA ATT AAC TCC GCC TTG AGA-3xe2x80x2 (SEQ ID NO:2), a Fla A gene sequence;
5xe2x80x2-CCT TCC TGT TGA ACA CCC TCT TGA AC-3xe2x80x2 (SEQ ID NO:3), a probe hybridizing to Fla A gene sequence;
5xe2x80x2-CTT GTA CCA GTT GTA CGG TCC-3xe2x80x2 (SEQ ID NO:4), a human placental DNA sequence suitable for use as a primer for internal positive control amplification;
5xe2x80x2-GGT AGC AGC GGT AGA GTT GTA-3xe2x80x2 (SEQ ID NO:5)), a human placental DNA sequence suitable for use as a primer for internal positive control amplification; and
5xe2x80x2-ATC ATG ATG TTC AAG TTG TGT TTT GC-3xe2x80x2 (SEQ ID NO:6), a human placental DNA sequence suitable for use as a probe for hybridizing to human placental DNA.
In preferred embodiments, one or more of the selected oligonucleotides can be conjugated to a detectable label, preferably a fluorescent dye, and most preferably a dye pair. Particularly preferred oligonucleotide dye conjugates are 5xe2x80x2-[6-carboxyfluorescein(FAM)]-CCT TCC TGT TGA ACA CCC TCT TGA AC-[6-carboxytetramethylrhodamine (TAMRA)]-3xe2x80x2 (SEQ ID NO:7); and 5xe2x80x2[2xe2x80x2-Chloro-7xe2x80x2-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC)]-ATC ATG ATG TTC AAG TTG TGT TTT GC-[6-carboxytetramethylrhodamine (TAMRA)]3xe2x80x2 (SEQ ID NO:8). These may be used as probes for FlaA gene and human placental DNA, respectively, in methods to detect the presence or amount of specific nucleic acids present in a test sample.
In another aspect, the present invention relates in part to methods that use primers to a sequence unrelated to Borrelia burgdorferi, e.g., human placental nucleic acid primers, to produce control amplicons as a positive assay control. In preferred embodiments, oligonucleotides having the sequences 5xe2x80x2-CTT GTA CCA GTT GTA CGG TCC-3xe2x80x2 (SEQ ID NO:4) and 5xe2x80x2-GGT AGC AGC GGT AGA GTT GTA-3xe2x80x2 (SEQ ID NO:5) are used as primers to amplify a sample of human placental nucleic acid to produce the control amplicons.
In various embodiments, control DNA, e.g., human placental DNA, can be spiked into a sample suspected to contain Borrelia burgdorferi, and two sets of primers, one set selected to amplify a control DNA sequence, and a second set selected to amplify a Borrelia burgdorferi sequence can be used during the amplification step. In these embodiments, amplification of the control DNA sequence can be detected as a positive control. If the control DNA is added prior to amplification, the positive control can signal successful amplification in samples negative for Borrelia burgdorferi. Alternatively, if the control DNA is added prior to nucleic acid isolation (which may occur prior to amplification), the positive control can signal both successful nucleic acid isolation and successful amplification.
In certain embodiments, FlaA-human placental hybrid amplicons can be prepared and purified for use in Borrelia burgdorferi assays. In these embodiments, hybrid amplicon nucleic acid can be prepared by including FlaA sequences in the control primers described above. These hybrid amplicons can then be introduced into a sample to be analyzed for the presence or amount of FlaA gene in the Borrelia burgdorferi gene sequence. Because of the flanking FlaA gene sequences present in the hybrid amplicon, primers can be selected that can amplify both the hybrid nucleic acid added, as well as any FlaA gene in the Borrelia burgdorferi gene sequence present in the sample. Depending on the timing at which the hybrid nucleic acid is introduced into the sample, the hybrid nucleic acid can serve as a positive control for nucleic acid extraction from the sample, and/or for an FlaA amplification reaction.
In another aspect, the present invention relates in part to methods for detecting the presence or amount of FlaA gene in the Borrelia burgdorferi gene sequence present in a test sample. The FlaA gene encodes the flagellin protein in the Borrelia burgdorferi gene sequence. These methods preferably comprise amplifying FlaA gene sequence if present in said sample using a pair of oligonucleotide primers; hybridizing said amplified FlaA gene with an oligonucleotide probe; and detecting a signal from said hybridized FlaA, wherein the signal is related to the presence or amount of FlaA gene in the Borrelia burgdorferi gene sequence in the test sample.
In various preferred embodiments, the oligonucleotide primers have the sequences 5xe2x80x2-TTG CAA ATC TTT TCT CTG GTG-3xe2x80x2 (SEQ ID NO:1) and 5xe2x80x2-AGA ATT AAC TCC GCC TTG AGA-3xe2x80x2 (SEQ ID NO:2), respectively; these primers hybridize to flanking regions on the FlaA gene. One of the primers anneals to base pairs 581-601 (from GenBank Accession# x15661) on the FlaA gene; the another anneals to base pairs 688-708 (from GenBank Accession# x15661) on the FlaA gene; the oligonucleotide probe can have the sequence 5xe2x80x2-CCT TCC TGT TGA ACA CCC TCT TGA AC-3xe2x80x2 (SEQ ID NO:3); which corresponds to base pairs 631-656 (from GenBank Accession# x15661); the oligonucleotide probe comprises a detectable label; the oligonucleotide probe has the sequence 5xe2x80x2(FAM)-CCT TCC TGT TGA ACA CCC TCT TGA AC-(TAMRA)3xe2x80x2 (SEQ ID NO:7); a positive control nucleic acid is introduced into the test sample prior to amplification of FlaA sequences; the positive control nucleic acid is human placental DNA; oligonucleotides having the sequences 5xe2x80x2- CTT GTA CCA GTT GTA CGG TCC-3xe2x80x2 (SEQ ID NO:4) and 5xe2x80x2-GGT AGC AGC GGT AGA GTT GTA-3xe2x80x2(SEQ ID NO:5) are used as primers to amplify a sample of human placental nucleic acid to produce positive control nucleic acid; the positive control nucleic acid is detectable using an oligonucleotide probe having the sequence 5xe2x80x2-ATC ATG ATG TTC AAG TTG TGT TTT GC-3xe2x80x2 (SEQ ID NO:6); and/or the positive control nucleic acid is detected using an oligonucleotide probe having the sequence 5xe2x80x2(VIC)-ATC ATG ATG TTC AAG TTG TGT TTT GC-(TAMRA)3xe2x80x2 (SEQ ID NO:8).
In yet another aspect of the present invention, a xe2x80x9creal time PCRxe2x80x9d assay providing dynamic fluorescence detection of amplified FlaA products produced in a PCR amplification reaction is described. During PCR, the amplified products hybridize to probe nucleic acids, which are labeled with both a reporter dye and a quencher dye. When these two dyes are in close proximity, i.e. both are present in an intact probe oligonucleotide, the fluorescence of the reporter dye is suppressed. However, a polymerase, such as AmpliTaq Gold(trademark), having 5xe2x80x2-3xe2x80x2 nuclease activity can be provided in the PCR reaction. This enzyme cleaves the fluorogenic probe if it is bound specifically to the target nucleic acid sequences between the priming sites. The reporter dye and quencher dye are separated upon cleavage, permitting fluorescent detection of the reporter dye. Upon excitation by a laser provided, e.g., by a sequencing apparatus, the fluorescent signal produced by the reporter dye is detected and/or quantified. The increase in fluorescence is a direct consequence of amplification of target nucleic acids during PCR.
In various preferred embodiments, the oligonucleotide primers used in the PCR amplification have the sequences 5xe2x80x2-TTG CAA ATC TTT TCT CTG GTG-3xe2x80x2 (SEQ ID NO:1) and 5xe2x80x2-AGA ATT AAC TCC GCC TTG AGA-3xe2x80x2 (SEQ ID NO:2); the reporter dye is FAM and the quencher dye is TAMRA; the FlaA oligonucleotide probe has the sequence 5xe2x80x2(FAM)-CCT TCC TGT TGA ACA CCC TCT TGA AC-(TAMRA)3xe2x80x2 (SEQ ID NO:7); a positive control nucleic acid is introduced into the test sample prior to PCR amplification of FlaA gene sequences; the positive control nucleic acid is human placental DNA; oligonucleotides having the sequences 5xe2x80x2-CTT GTA CCA GTT GTA CGG TCC-3xe2x80x2 (SEQ ID NO:4) and 5xe2x80x2-GGT AGC AGC GGT AGA GTT GTA-3xe2x80x2 (SEQ ID NO:5) are used as primers to amplify a sample of human placental nucleic acid to produce positive control nucleic acid; the positive control nucleic acid is amplified by the same primers used to amplify the FlaA gene sequences; the reporter dye is VIC and the quencher dye is TAMRA; and/or the positive control nucleic acid is detected using an oligonucleotide probe having the sequence 5xe2x80x2(VIC)-ATC ATG ATG TTC AAG TTG TGT TTT GC-(TAMRA)3xe2x80x2 (SEQ ID NO:8).
In yet another aspect, the methods and compositions for detecting and/or quantifying Borrelia burgdorferi gene of the present invention can be used for designing a treatment regimen. In particular, the detection of the presence or amount of Borrelia burgdorferi nucleic acid in a biological sample following a selected treatment(s) can be used to assess the success or lack thereof in the treatment regimen. The present invention can also be used to compare the relative presence or amount of Borrelia burgdorferi nucleic acids in a patient before and after such a treatment regimen. Similarly, methods and compositions described herein can be used for screening therapeutic compounds. In particular, the quantitative detection of the presence or amount of Borrelia burgdorferi nucleic acids in a biological sample following administration of one or more compounds can be used to assess therapeutic efficacy. The present invention can also be used to compare the relative presence or amount of Borrelia burgdorferi nucleic acids in a patient before and after administration of one or more compounds.
In another aspect, the present invention relates in part to kits comprising sufficient materials for performing one or more methods described herein. In preferred embodiments, a kit includes one or more materials selected from the following group in an amount sufficient to perform at least one Borrelia burgdorferi assay: Oligonucleotide primers having the sequences 5xe2x80x2-TTG CAA ATC TTT TCT CTG GTG-3xe2x80x2 (SEQ ID NO:1) and 5xe2x80x2-AGA ATT AAC TCC GCC TTG AGA-3xe2x80x2 (SEQ ID NO:2); an oligonucleotide probe having the sequence 5xe2x80x2-CCT TCC TGT TGA ACA CCC TCT TGA AC-3xe2x80x2 (SEQ ID NO:3); an oligonucleotide probe having the sequence 5xe2x80x2(FAM)-CCT TCC TGT TGA ACA CCC TCT TGA AC-(TAMRA)3xe2x80x2 (SEQ ID NO:7); a positive control nucleic acid to be introduced into a test sample prior to amplification of FlaA gene sequences; a positive control nucleic acid that is human placental DNA; oligonucleotides having the sequences 5xe2x80x2-CTT GTA CCA GTT GTA CGG TCC-3xe2x80x2 (SEQ ID NO:4) and 5xe2x80x2-GGT AGC AGC GGT AGA GTT GTA-3xe2x80x2 (SEQ ID NO:5) to be used as primers to amplify a sample of human placental nucleic acid to produce positive control nucleic acid; a positive control nucleic acid that is detectable using an oligonucleotide probe having the sequence 5xe2x80x2-ATC ATG ATG TTC AAG TTG TGT TTT GC-3xe2x80x2 (SEQ ID NO:6); a positive control nucleic acid that is detected using an oligonucleotide probe having the sequence 5xe2x80x2(VIC)-ATC ATG ATG TTC AAG TTG TGT TTT GC-(TAMRA)3xe2x80x2 (SEQ ID NO:8); and/or an oligonucleotide probe having the sequence 5xe2x80x2(VIC)-ATC ATG ATG TTC AAG TTG TGT TTT GC-(TAMRA)3xe2x80x2 (SEQ ID NO:8).
The present invention provides methods and compositions for the rapid and sensitive determination of Borrelia burgdorferi nucleic acids in test samples. In particular, oligonucleotide probes and primers are described that can be used for quantitatively or qualitatively detecting FlaA gene sequence encoding the flagellin protein on the Borrelia burgdorferi gene sequence in a sample. The present invention also provides primers and probes for generating and detecting control nucleic acid sequences that provide a convenient method for assessing internal quality control of the Borrelia burgdorferi assay.
As used herein, the term xe2x80x9cFlaA-human placental nucleic acid hybridsxe2x80x9d refers to chimeric nucleic acid molecules containing both FlaA gene sequences and human placental nucleic acids sequences. Preferred FlaA-human placental hybrids comprise a core sequence from human placental DNA, flanked by FlaA sequences having sufficient length to hybridize to amplification primers. Preferably, the FlaA-human placental hybrid comprises at least 3 consecutive bases from an FlaA sequence, more preferably at least 5 consecutive bases from an FlaA sequence, even more preferably at least 10 consecutive bases from an FlaA sequence, and most preferably at least 20 consecutive bases from an FlaA sequence.
As used herein, the term xe2x80x9cpurifiedxe2x80x9d in reference to oligonucleotides does not require absolute purity. Instead, it represents an indication that the sequence is relatively more pure than in the natural environment. Such oligonucleotides may be obtained by a number of methods including, for example, laboratory synthesis, restriction enzyme digestion or PCR. A xe2x80x9csubstantially purifiedxe2x80x9d oligonucleotide is preferably greater than 50% pure, more preferably at least 75% pure, and most preferably at least 95% pure.
As used herein, the term xe2x80x9coligonucleotidesxe2x80x9d refers to a short polymer composed of deoxyribonucleotides, ribonucleotides or any combination thereof. These oligonucleotides are at least 9 nucleotides in length, preferably 20 to 50 nucleotide long, with 21 to 26 nucleotides being the most common. In certain embodiments, the oligonucleotides are jointed together with a detectable label.
As used herein, the term xe2x80x9cBorrelia burgdorferi nucleic acidsxe2x80x9d and/or Borrelia burgdorferi gene sequence refer to DNA and/or RNA comprising a contiguous sequence from Borrelia burgdorferi genome, or the complement thereof. Borrelia burgdorferi nucleic acids and/or gene sequence may be Borrelia burgdorferi genomic DNA, Borrelia burgdorferi messenger RNA, or the complement of these sources, obtained by any method including obtaining the nucleic acid from a biological source, synthesizing the nucleic acid in vitro, or amplifying the nucleic acid by any method known in the art.
As used herein, the term xe2x80x9chybridizexe2x80x9d refers to process that two complementary nucleic acid strands anneal to each other under appropriately stringent conditions. Hybridizations are typically and preferably conducted with probe-length nucleic acid molecules, preferably 20-100 nucleotides in length. Nucleic acid hybridization techniques are well known in the art. See, e.g., Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y. Those skilled in the art understand how to estimate and adjust the stringency of hybridization conditions such that sequences having at least a desired level of complementarity will stably hybridize, while those having lower complementarity will not. For examples of hybridization conditions and parameters, see, e.g., Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y.; Ausubel, F. M. et al. 1994, Current Protocols in Molecular Biology. John Wiley and Sons, Secaucus, N.J.
The term xe2x80x9cstringent hybridization conditionsxe2x80x9d as used herein refers to hybridization conditions at least as stringent as the following: hybridization in 50% formamide, 5xc3x97SSC, 50 mM NaH2PO4, pH 6.8, 0.5% SDS, 0.1 mg/ml sonicated salmon sperm DNA, and 5xc3x97Denhart""s solution at 42xc2x0 C. overnight; washing with 2xc3x97SSC, 0.1% SDS at 45xc2x0 C.; and washing with 0.2xc3x97SSC, 0.1% SDS at 45xc2x0 C. In another example, stringent hybridization conditions should not allow for hybridization of two nucleic acids which differ over a stretch of 20 contiguous nucleotides by more than two bases.
The term xe2x80x9camplifyxe2x80x9d with respect to nucleic acid sequences refers to methods that increase the representation of a population of nucleic acid sequences in a sample. Nucleic acid amplification methods, such as PCR, isothermal methods, rolling circle methods, etc., are well known to the skilled artisan. See, e.g., Saiki, xe2x80x9cAmplification of Genomic DNAxe2x80x9d in PCR Protocols, Innis et al., Eds., Academic Press, San Diego, Calif. 1990, pp 13-20; Wharam et al., Nucleic Acids Res. Jun. 1, 2001;29(11):E54-E54; Hafner et al., Biotechniques April 2001;30(4):852-6, 858, 860 passim; Zhong et al., Biotechniques April 2001;30(4):852-6, 858, 860 passim.
As used herein, the term xe2x80x9ctest samplexe2x80x9d refers to any liquid or solid material believed to comprise Borrelia burgdorferi nucleic acids. In preferred embodiments, a test sample is obtained from a biological source, such as cells in culture or a tissue sample from an animal, most preferably, a human. Preferred sample tissues of the instant invention include, but are not limited to, plasma, serum, whole blood, blood cells, lymphatic fluid, cerebrospinal fluid, synovial fluid, urine, saliva, and skin or other organs (e.g. biopsy material). The term xe2x80x9cpatient samplexe2x80x9d as used herein refers to a tissue sample obtained from a human seeking diagnosis or treatment of a disease related to a Borrelia burgdorferi infection.
The term xe2x80x9cdetectable labelxe2x80x9d as used herein refers to a composition or moiety that is detectable by spectroscopic, photochemical, biochemical, immunochemical, electromagnetic, radiochemical, or chemical means such as fluorescence, chemifluoresence, or chemiluminescence, or any other appropriate means. Preferred detectable labels are fluorescent dye molecules, or fluorochromes, such fluorescein, phycoerythrin, CY3, CY5, allophycocyanine, Texas Red, peridenin chlorophyll, cyanine, FAM, JOE, TAMRA, tandem conjugates such as phycoerythrin-CY5, and the like. These examples are not meant to be limiting. Methods and compositions for detectably labeling molecules, such as oligonucleotides, PNA-DNA hybrids, etc. are well known in the art. See, e.g., U.S. Pat. Nos. 6,316,230; 6,297,016; 6,316,610; 6,060,240; 6,150,107; and 6,028,290, each of which are hereby incorporated by reference in their entirety.
The term xe2x80x9cfluorochromexe2x80x9d as used herein refers to a molecule that absorbs a quantum of electromagnetic radiation at one wavelength, and emits one or more photons at a different, typically longer, wavelength in response. In preferred embodiments, a fluorochrome can be a member of a pair of physically linked fluorochromes that exhibit fluorescence energy transfer. An energy transfer pair may be excited by a quantum of electromagnetic radiation at a wavelength at which the donor fluorochrome is excited; however, fluorescence from the donor fluorochrome that would be expected in the absence of the acceptor is quenched at least in part, and emission at an emission wavelength of the acceptor fluorochrome is observed.
In particularly preferred embodiments, a fluorochrome is one member of a physically linked xe2x80x9cmolecular beaconxe2x80x9d pair. In these embodiments, the molecular beacon pair may be excited by a quantum of electromagnetic radiation at a wavelength at which a first fluorochrome member of the pair is excited; however, fluorescence from the first fluorochrome that would be expected in the absence of the second fluorochrome is quenched at least in part. Unlike energy transfer pairs, however, emission at an emission wavelength of the acceptor fluorochrome is not observed. Thus, these labels comprise a pair of dyes, one of which is referred to as a xe2x80x9creporter,xe2x80x9d and the second of which is referred to as a xe2x80x9cquencher.xe2x80x9d When the two dyes are held in close proximity, such as at the ends of a nucleic acid probe, the quencher moiety prevents detection of a fluorescent signal from the reporter moiety. When the two dyes are separated, however, the fluorescent signal from the reporter moiety becomes detectable.
The term xe2x80x9clinkerxe2x80x9d as used herein refers to one or more chemical bonds or a chemical group used to link one moiety to another, serving as a divalent bridge, where it provides a group between two other chemical moieties.
Sample Preparation
The presence or amount of Borrelia burgdorferi nucleic acids in a sample can be determined by amplifying one or more target regions, such as nucleotides in the FlaA gene, within the Borrelia burgdorferi genome. Thus, any liquid or solid material believed to comprise Borrelia burgdorferi nucleic acids can be an appropriate sample. Preferred sample tissues include plasma, serum, whole blood, blood cells, lymphatic fluid, cerebral spinal fluid, synovial fluid and others.
Such samples will often be taken from patients suspected of having Borrelia burgdorferi infection, or having a clinical manifestations of Lyme disease. Nucleic acids representing Borrelia burgdorferi may be extracted from tissue samples. Various commercial nucleic acid purification/extraction systems and kits are known to the skilled artisan, and used to isolate Borrelia burgdorferi nucleic acids from samples. For example, the MagNA Pure automated extraction system may be used for all specimen types. The MagNA Pure system is used for simultaneous extraction of all specimens with a single protocol using the system""s MagNA Pure LC DNA isolation Kit I.
Amplification of Borrelia burgdorferi Nucleic Acids
Target samples or isolated nucleic acids may be amplified by various methods known to the skilled artisan. Preferably, PCR is used to amplify Borrelia burgdorferi nucleic acids. In this method, two or more oligonucleotide primers that flank and bind to opposite strands of a target sequence are repetitively annealed to their complementary sequences, extended by a DNA polymerase, and heat denatured, resulting in exponential amplification of the target nucleic acid sequences. The skilled artisan is capable of designing and preparing primers that are appropriate for amplifying a target sequence. In preferred embodiment of the instant invention, primers are designed for amplifying all or a part of the FlaA gene of Borrelia burgdorferi. These primers hybridize to flanking regions on the FlaA gene encoding the flagellin protein. The primers amplify the regions of 581-708 bp on the FlaA gene (from GenBank accession number x15661). Cycling parameters can be varied, depending on the length of nucleic acids to be extended.
Hybridization Probes With a Detectable Label
Oligonucleotide probes complementary and hybridizing to the amplified target nucleic acids may be conjugated to a detectable label. Preferably, the detectable label is a fluorescent dye. Particularly preferred are detectable labels known as xe2x80x9cmolecular beacons.xe2x80x9d These labels comprise a pair of dyes, one of which is referred to as a xe2x80x9creporter,xe2x80x9d and the second of which is referred to as a xe2x80x9cquencher.xe2x80x9d When the two dyes are held in close proximity, such as at the ends of a nucleic acid probe, the quencher moiety prevents detection of a fluorescent signal from the reporter moiety. When the two dyes are separated, however, the fluorescent signal from the reporter moiety becomes detectable.
Molecular beacons can be utilized during PCR, for example, by using a DNA polymerase that cleaves a probe nucleic acid if it is bound specifically to the target nucleic acid sequence. Quantitative real-time PCR is based on detection of a fluorescent signal produced proportionally during the amplification of a PCR product. A probe is designed to anneal to the target sequence between the traditional forward and reverse primers. The probe is labeled at the 5xe2x80x2 end with a reporter fluorochrome, and a quencher fluorochrome is added at any other position (or at the 3xe2x80x2 end). The probe is designed to have a higher Tm than the primers. As long as both fluorochromes are on the probe, the quencher molecule stops all fluorescence by the reporter. However, as Taq polymerase extends the primer, the intrinsic 5xe2x80x2 to 3xe2x80x2 nuclease activity of Taq degrades the probe, releasing the reporter fluorochrome. The amount of fluorescence released during the amplification cycle is proportional to the amount of product generated in each cycle. See, e.g., van Schie et al., Biotechniques 29: 1296-1300 (2000).
Methods for attaching detectable labels are well known in the art. See, e.g., Chu et al., Methods Mol. Biol. 26, 145-165 (1994); Hileman et al., Bioconjug. Chem. 5, 436-444 (1994).
In preferred embodiment of the instant invention, the oligonucleotide probe hybridizes to the amplified FlaA gene sequence. The probe corresponds to 631-656 bp of FlaA gene (from GenBank accession number x15661), and is attached to a pair of detectable labels.
Preparation of an Internal Control
As a quality control measure, an internal amplification control may be included in one or more samples to be extracted and amplified. While human placental nucleic acid control sequences are described herein, the skilled artisan will understand that any detectable sequence that is not derived from Borrelia burgdorferi can be used as the control sequence. A control sequence can be produced synthetically, but is preferably produced by amplifying the control sequence, e.g., human placental DNA, using a pair of human placental primer sequences. In particularly preferred embodiments, a control primer is a hybrid nucleic acid comprising human placental sequence flanked by FlaA primer target sequences. Sequences amplified using these hybrid nucleic acids comprise a human placental sequence flanked by sequences that hybridize to FlaA primer sequences These controls can be mixed with sample (or purified nucleic acids isolated from the sample), and amplified with sample nucleic acids using a pair of FlaA primers. If PCR amplification is successful, the internal amplification control amplicons can then be detected and differentiated from FlaA sequences using a probe to the human placental sequence. Additionally, if included in the sample prior to purification of nucleic acids, the control sequences can also act as a positive purification control.
Borrelia burgdorferi Assay
In preferred embodiments, the FlaA gene specific primers are shown in SEQ ID:1 and SEQ ID:2, although the skilled artisan will understand that other probes may be used. Stock Borrelia burgdorferi standard curve dilutions may be run simultaneously. The methods described herein can provide qualitative and quantitative results up to about 5,000 Borrelia burgdorferi organisms per reaction.
To minimize the potential for cross contamination, reagent and master mix preparation, specimen processing and PCR setup, amplification and detection are conducted in physical separated areas.